Abstract
Recent evidence indicates that regulatory small non-coding RNAs are not only components of eukaryotic cells and vesicles, but also reside within a number of different viruses including retroviral particles. Using ultra-deep sequencing we have comprehensively analyzed the content of simian immunodeficiency virions (SIV), which were compared to mock-control preparations. Our analysis revealed that more than 428,000 sequence reads matched the SIV mac239 genome sequence. Among these we could identify 12 virus-derived small RNAs (vsRNAs) that were highly abundant. Beside known retrovirus-enriched small RNAs, like 7SL-RNA, tRNALys3 and tRNALys isoacceptors, we also identified defined fragments derived from small ILF3/NF90-associated RNA snaR-A14, that were enriched more than 50 fold in SIV. We also found evidence that small nucleolar RNAs U2 and U12 were underrepresented in the SIV preparation, indicating that the relative number or the content of co-isolated exosomes was changed upon infection. Our comprehensive atlas of SIV-incorporated small RNAs provides a refined picture of the composition of retrovirions, which gives novel insights into viral packaging.
Highlights
Within the last decade, a diverse class of non-coding RNA molecules was found to orchestrate a large number of physiological processes
Packaging of small RNAs into virions is a common feature known from DNA [23,24,25,26] and RNA viruses [17,27]
To determine whether other small RNAs are packaged into retroviral particles we analysed the small RNA content of simian immunodeficiency virions (SIV) by ultra-deep sequencing
Summary
A diverse class of non-coding RNA molecules (ncRNAs) was found to orchestrate a large number of physiological processes. The most prominent population of ncRNAs was referred to as microRNAs (miRNAs) that induce gene silencing by translational repression or mRNA decay [1]. Derived from primary transcripts, biogenesis of miRNAs starts with a precursor molecule (pri-miRNAs) that is processed by the nuclear RNase III enzyme Drosha. The pre-miRNA is cleaved by the cytoplasmic RNase III enzyme Dicer that produces the mature miRNA of around 22 nt in length. To exert their function, miRNAs are incorporated into the RNA-induced silencing complex (RISC). Complementary binding of the miRNAs to its respective target transcripts leads to mRNA degradation or translational repression, influencing physiological or promoting pathological processes. The function of these fragments in Hepatitis C-, Vesicular Stomatitis-, West Nile-, Dengue-, and Polio-virus infected cells remains unknown [3]
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